Not sure, because I just noticed it the other day. I don't believe equipment caused it, though. Haven't put a single point of karma into nuyen. As a result, he's just under -250,000 in nuyen, but I'm pretty sure he's supposed to be that way. I was under the impression 'ware and equipment was provided by TriSeq (if not, Omar is well and truly FUBAR). It's probably a combination of:
-Buying up Magic, then slapping on 'ware, and Chummer freaking out
-Not paying the karma cost for the bonded foci.
I'm not familiar with karmagen, so I don't think that accounts for anywhere near -68 karma Omeed has. Other than those two things, I'm pretty clueless as to what could've caused this, but I can always pare down his skills. I'm starting to think I might have an easier time building him again from scratch.
EDIT: I remember at one point our GM said; "You guys can take/would've had time to Initiate." This is another thing I probably just sort of threw on without really thinking about it, probably forgot to pay karma for this as well.